BamTools  2.5.1
Classes | Namespaces | Typedefs | Functions
BamAux.h File Reference
#include <cstddef>
#include <cstring>
#include <fstream>
#include <iostream>
#include <string>
#include <vector>
#include "api/api_global.h"

Go to the source code of this file.

Classes

struct  BamTools::CigarOp
 Represents a CIGAR alignment operation. More...
 
struct  BamTools::RefData
 Represents a reference sequence entry. More...
 
struct  BamTools::BamRegion
 Represents a sequential genomic region. More...
 
struct  BamTools::CustomHeaderTag
 

Namespaces

 BamTools
 Contains all BamTools classes & methods.
 

Typedefs

typedef std::vector< RefData > BamTools::RefVector
 convenience typedef for vector of RefData entries More...
 

Functions

API_EXPORT bool BamTools::FileExists (const std::string &filename)
 returns true if the file exists More...
 
API_EXPORT void BamTools::SwapEndian_16 (int16_t &x)
 swaps endianness of signed 16-bit integer, in place More...
 
API_EXPORT void BamTools::SwapEndian_16 (uint16_t &x)
 swaps endianness of unsigned 16-bit integer, in place More...
 
API_EXPORT void BamTools::SwapEndian_32 (int32_t &x)
 swaps endianness of signed 32-bit integer, in place More...
 
API_EXPORT void BamTools::SwapEndian_32 (uint32_t &x)
 swaps endianness of unsigned 32-bit integer, in place More...
 
API_EXPORT void BamTools::SwapEndian_64 (int64_t &x)
 swaps endianness of signed 64-bit integer, in place More...
 
API_EXPORT void BamTools::SwapEndian_64 (uint64_t &x)
 swaps endianness of unsigned 64-bit integer, in place More...
 
API_EXPORT void BamTools::SwapEndian_16p (char *data)
 swaps endianness of the next 2 bytes in a buffer, in place More...
 
API_EXPORT void BamTools::SwapEndian_32p (char *data)
 swaps endianness of the next 4 bytes in a buffer, in place More...
 
API_EXPORT void BamTools::SwapEndian_64p (char *data)
 swaps endianness of the next 8 bytes in a buffer, in place More...
 
API_EXPORT bool BamTools::SystemIsBigEndian ()
 checks host architecture's byte order More...
 
API_EXPORT void BamTools::PackUnsignedInt (char *buffer, unsigned int value)
 stores unsigned integer value in a byte buffer More...
 
API_EXPORT void BamTools::PackUnsignedShort (char *buffer, unsigned short value)
 stores unsigned short integer value in a byte buffer More...
 
API_EXPORT double BamTools::UnpackDouble (const char *buffer)
 reads a double value from byte buffer More...
 
API_EXPORT double BamTools::UnpackDouble (char *buffer)
 reads a double value from byte buffer More...
 
API_EXPORT float BamTools::UnpackFloat (const char *buffer)
 reads a float value from byte buffer More...
 
API_EXPORT float BamTools::UnpackFloat (char *buffer)
 reads a float value from byte buffer More...
 
API_EXPORT signed int BamTools::UnpackSignedInt (const char *buffer)
 reads a signed integer value from byte buffer More...
 
API_EXPORT signed int BamTools::UnpackSignedInt (char *buffer)
 reads a signed integer value from byte buffer More...
 
API_EXPORT signed short BamTools::UnpackSignedShort (const char *buffer)
 reads a signed short integer value from byte buffer More...
 
API_EXPORT signed short BamTools::UnpackSignedShort (char *buffer)
 reads a signed short integer value from byte buffer More...
 
API_EXPORT unsigned int BamTools::UnpackUnsignedInt (const char *buffer)
 reads an unsigned integer value from byte buffer More...
 
API_EXPORT unsigned int BamTools::UnpackUnsignedInt (char *buffer)
 reads an unsigned integer value from byte buffer More...
 
API_EXPORT unsigned short BamTools::UnpackUnsignedShort (const char *buffer)
 reads an unsigned short integer value from byte buffer More...
 
API_EXPORT unsigned short BamTools::UnpackUnsignedShort (char *buffer)
 reads an unsigned short integer value from byte buffer More...
 

Detailed Description

Provides data structures & utility methods that are used throughout the API.